Starting phenix.real_space_refine on Tue Feb 3 17:36:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9shp_54907/02_2026/9shp_54907.cif Found real_map, /net/cci-nas-00/data/ceres_data/9shp_54907/02_2026/9shp_54907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9shp_54907/02_2026/9shp_54907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9shp_54907/02_2026/9shp_54907.map" model { file = "/net/cci-nas-00/data/ceres_data/9shp_54907/02_2026/9shp_54907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9shp_54907/02_2026/9shp_54907.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 3529 2.51 5 N 960 2.21 5 O 1026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5554 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 5428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5428 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 657} Chain breaks: 4 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 154 Planarities with less than four sites: {'ARG:plan': 12, 'PHE:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 6, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 147 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'RNA': 6} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.39, per 1000 atoms: 0.25 Number of scatterers: 5554 At special positions: 0 Unit cell: (72.8584, 76.9825, 118.223, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 6 15.00 Mg 1 11.99 O 1026 8.00 N 960 7.00 C 3529 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 361.2 milliseconds 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1310 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 31.7% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 143 through 150 removed outlier: 3.507A pdb=" N LEU B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 208 through 223 removed outlier: 4.051A pdb=" N ASN B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 299 through 305 Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 400 through 412 removed outlier: 3.610A pdb=" N MET B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N HIS B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 removed outlier: 3.938A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 423 " --> pdb=" O GLN B 419 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG B 424 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 441 removed outlier: 3.630A pdb=" N ASP B 441 " --> pdb=" O ARG B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 518 removed outlier: 4.353A pdb=" N SER B 511 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 524 removed outlier: 3.784A pdb=" N MET B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.712A pdb=" N LEU B 546 " --> pdb=" O TYR B 542 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 579 removed outlier: 3.679A pdb=" N CYS B 577 " --> pdb=" O LYS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.548A pdb=" N LEU B 607 " --> pdb=" O THR B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 691 removed outlier: 3.520A pdb=" N VAL B 678 " --> pdb=" O ASP B 674 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS B 679 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 684 " --> pdb=" O LEU B 680 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG B 685 " --> pdb=" O GLN B 681 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY B 689 " --> pdb=" O ARG B 685 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N CYS B 690 " --> pdb=" O ALA B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 removed outlier: 3.600A pdb=" N VAL B 714 " --> pdb=" O LEU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 725 Processing helix chain 'B' and resid 805 through 816 removed outlier: 3.568A pdb=" N ILE B 809 " --> pdb=" O LYS B 805 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 810 " --> pdb=" O PRO B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 819 No H-bonds generated for 'chain 'B' and resid 817 through 819' Processing helix chain 'B' and resid 830 through 846 Processing sheet with id=AA1, first strand: chain 'B' and resid 452 through 456 Processing sheet with id=AA2, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.547A pdb=" N LEU B 266 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 265 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 124 removed outlier: 3.560A pdb=" N THR B 123 " --> pdb=" O SER B 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 171 removed outlier: 3.597A pdb=" N THR B 197 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 192 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER B 184 " --> pdb=" O VAL B 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 227 through 229 removed outlier: 4.013A pdb=" N TRP B 250 " --> pdb=" O LYS B 273 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS B 273 " --> pdb=" O TRP B 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 309 through 310 Processing sheet with id=AA7, first strand: chain 'B' and resid 463 through 464 removed outlier: 3.675A pdb=" N ILE B 463 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 531 through 534 removed outlier: 3.700A pdb=" N ILE B 533 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 558 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 557 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL B 587 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N CYS B 559 " --> pdb=" O VAL B 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 659 through 664 removed outlier: 3.743A pdb=" N VAL B 649 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY B 631 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE B 629 " --> pdb=" O SER B 651 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N MET B 628 " --> pdb=" O ILE B 699 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N TYR B 701 " --> pdb=" O MET B 628 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL B 630 " --> pdb=" O TYR B 701 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 738 " --> pdb=" O ILE B 798 " (cutoff:3.500A) 170 hydrogen bonds defined for protein. 465 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1781 1.34 - 1.46: 1006 1.46 - 1.57: 2834 1.57 - 1.69: 11 1.69 - 1.81: 48 Bond restraints: 5680 Sorted by residual: bond pdb=" N LYS B 612 " pdb=" CA LYS B 612 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.29e+00 bond pdb=" P U C 1 " pdb=" OP3 U C 1 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.31e+00 bond pdb=" P C C 4 " pdb=" OP2 C C 4 " ideal model delta sigma weight residual 1.485 1.521 -0.036 2.00e-02 2.50e+03 3.21e+00 bond pdb=" O5' C C 4 " pdb=" C5' C C 4 " ideal model delta sigma weight residual 1.420 1.445 -0.025 1.50e-02 4.44e+03 2.75e+00 bond pdb=" P U C 1 " pdb=" OP2 U C 1 " ideal model delta sigma weight residual 1.485 1.518 -0.033 2.00e-02 2.50e+03 2.73e+00 ... (remaining 5675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 7615 1.95 - 3.91: 99 3.91 - 5.86: 22 5.86 - 7.81: 5 7.81 - 9.76: 3 Bond angle restraints: 7744 Sorted by residual: angle pdb=" C TYR B 861 " pdb=" N LEU B 862 " pdb=" CA LEU B 862 " ideal model delta sigma weight residual 121.70 128.79 -7.09 1.80e+00 3.09e-01 1.55e+01 angle pdb=" O3' C C 4 " pdb=" P C C 5 " pdb=" O5' C C 5 " ideal model delta sigma weight residual 104.00 98.14 5.86 1.50e+00 4.44e-01 1.52e+01 angle pdb=" CB MET B 284 " pdb=" CG MET B 284 " pdb=" SD MET B 284 " ideal model delta sigma weight residual 112.70 122.46 -9.76 3.00e+00 1.11e-01 1.06e+01 angle pdb=" CA PRO B 806 " pdb=" N PRO B 806 " pdb=" CD PRO B 806 " ideal model delta sigma weight residual 112.00 107.77 4.23 1.40e+00 5.10e-01 9.14e+00 angle pdb=" OG1 THR B 771 " pdb=" CB THR B 771 " pdb=" CG2 THR B 771 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.95e+00 ... (remaining 7739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 2842 16.95 - 33.91: 413 33.91 - 50.86: 138 50.86 - 67.82: 26 67.82 - 84.77: 8 Dihedral angle restraints: 3427 sinusoidal: 1401 harmonic: 2026 Sorted by residual: dihedral pdb=" CA TRP B 659 " pdb=" C TRP B 659 " pdb=" N PHE B 660 " pdb=" CA PHE B 660 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CG ARG B 147 " pdb=" CD ARG B 147 " pdb=" NE ARG B 147 " pdb=" CZ ARG B 147 " ideal model delta sinusoidal sigma weight residual 180.00 135.46 44.54 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU B 616 " pdb=" CG GLU B 616 " pdb=" CD GLU B 616 " pdb=" OE1 GLU B 616 " ideal model delta sinusoidal sigma weight residual 0.00 -84.77 84.77 1 3.00e+01 1.11e-03 9.69e+00 ... (remaining 3424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 883 0.118 - 0.235: 15 0.235 - 0.353: 0 0.353 - 0.471: 0 0.471 - 0.588: 2 Chirality restraints: 900 Sorted by residual: chirality pdb=" P U C 1 " pdb=" OP1 U C 1 " pdb=" OP2 U C 1 " pdb=" O5' U C 1 " both_signs ideal model delta sigma weight residual True 2.41 3.00 -0.59 2.00e-01 2.50e+01 8.66e+00 chirality pdb=" P C C 4 " pdb=" OP1 C C 4 " pdb=" OP2 C C 4 " pdb=" O5' C C 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.25e+00 chirality pdb=" CB THR B 771 " pdb=" CA THR B 771 " pdb=" OG1 THR B 771 " pdb=" CG2 THR B 771 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 897 not shown) Planarity restraints: 962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 805 " -0.063 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO B 806 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO B 806 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 806 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 622 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO B 623 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 623 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 623 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 125 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO B 126 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " 0.021 5.00e-02 4.00e+02 ... (remaining 959 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 37 2.50 - 3.10: 3867 3.10 - 3.70: 8252 3.70 - 4.30: 11240 4.30 - 4.90: 18504 Nonbonded interactions: 41900 Sorted by model distance: nonbonded pdb=" NE2 GLN B 608 " pdb="MG MG B 901 " model vdw 1.896 2.250 nonbonded pdb=" OE1 GLN B 585 " pdb="MG MG B 901 " model vdw 2.125 2.170 nonbonded pdb=" O ILE B 809 " pdb=" OG1 THR B 813 " model vdw 2.214 3.040 nonbonded pdb=" O LEU B 516 " pdb=" OG1 THR B 520 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASN B 505 " pdb=" OG SER B 562 " model vdw 2.253 3.040 ... (remaining 41895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.120 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 5680 Z= 0.151 Angle : 0.618 9.764 7744 Z= 0.318 Chirality : 0.051 0.588 900 Planarity : 0.005 0.094 962 Dihedral : 18.124 84.770 2117 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.51 % Allowed : 33.62 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.31), residues: 680 helix: -0.53 (0.38), residues: 175 sheet: -2.24 (0.42), residues: 142 loop : -1.54 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 420 TYR 0.010 0.001 TYR B 776 PHE 0.016 0.002 PHE B 778 TRP 0.011 0.001 TRP B 442 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5680) covalent geometry : angle 0.61848 ( 7744) hydrogen bonds : bond 0.29219 ( 170) hydrogen bonds : angle 9.41250 ( 465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.0913 time to fit residues: 5.7072 Evaluate side-chains 39 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 767 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 HIS B 852 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.084849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.074185 restraints weight = 25510.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.075825 restraints weight = 15005.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.077025 restraints weight = 10226.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.077855 restraints weight = 7683.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.078497 restraints weight = 6202.038| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5680 Z= 0.131 Angle : 0.567 7.374 7744 Z= 0.295 Chirality : 0.044 0.142 900 Planarity : 0.004 0.049 962 Dihedral : 9.039 73.140 845 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.74 % Allowed : 33.79 % Favored : 62.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.30), residues: 680 helix: -0.27 (0.37), residues: 190 sheet: -2.11 (0.44), residues: 132 loop : -1.52 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 504 TYR 0.012 0.001 TYR B 575 PHE 0.014 0.001 PHE B 470 TRP 0.012 0.001 TRP B 687 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5680) covalent geometry : angle 0.56730 ( 7744) hydrogen bonds : bond 0.04804 ( 170) hydrogen bonds : angle 6.07489 ( 465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: B 224 MET cc_start: 0.8280 (mtm) cc_final: 0.8031 (ptp) REVERT: B 622 MET cc_start: 0.6968 (ppp) cc_final: 0.6559 (pmm) REVERT: B 732 TYR cc_start: 0.4301 (OUTLIER) cc_final: 0.3081 (m-80) outliers start: 22 outliers final: 5 residues processed: 64 average time/residue: 0.0731 time to fit residues: 6.3087 Evaluate side-chains 42 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 732 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 0.0980 chunk 5 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.085592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.075074 restraints weight = 24798.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.076747 restraints weight = 14402.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.077958 restraints weight = 9757.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.078810 restraints weight = 7299.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.079380 restraints weight = 5853.587| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5680 Z= 0.103 Angle : 0.557 11.762 7744 Z= 0.273 Chirality : 0.043 0.139 900 Planarity : 0.004 0.037 962 Dihedral : 8.472 73.139 839 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.06 % Allowed : 34.47 % Favored : 62.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.30), residues: 680 helix: -0.02 (0.37), residues: 195 sheet: -2.07 (0.43), residues: 132 loop : -1.65 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 420 TYR 0.013 0.001 TYR B 575 PHE 0.012 0.001 PHE B 470 TRP 0.008 0.001 TRP B 687 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 5680) covalent geometry : angle 0.55706 ( 7744) hydrogen bonds : bond 0.04204 ( 170) hydrogen bonds : angle 5.38292 ( 465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: B 224 MET cc_start: 0.8181 (mtm) cc_final: 0.7871 (ptp) REVERT: B 532 MET cc_start: 0.8194 (mmm) cc_final: 0.7954 (mmm) REVERT: B 622 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6750 (pmm) REVERT: B 725 LEU cc_start: 0.7115 (tp) cc_final: 0.6832 (tt) REVERT: B 732 TYR cc_start: 0.3740 (OUTLIER) cc_final: 0.2531 (m-80) outliers start: 18 outliers final: 8 residues processed: 55 average time/residue: 0.0537 time to fit residues: 4.2053 Evaluate side-chains 46 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 732 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN ** B 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.084742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.074208 restraints weight = 25560.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.075809 restraints weight = 15126.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.076964 restraints weight = 10404.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.077685 restraints weight = 7846.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.078291 restraints weight = 6408.413| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5680 Z= 0.126 Angle : 0.541 11.046 7744 Z= 0.271 Chirality : 0.043 0.135 900 Planarity : 0.004 0.038 962 Dihedral : 8.381 73.256 839 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.92 % Allowed : 33.28 % Favored : 61.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.30), residues: 680 helix: 0.05 (0.37), residues: 194 sheet: -2.02 (0.40), residues: 148 loop : -1.62 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 218 TYR 0.014 0.001 TYR B 575 PHE 0.016 0.001 PHE B 470 TRP 0.006 0.001 TRP B 823 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5680) covalent geometry : angle 0.54057 ( 7744) hydrogen bonds : bond 0.03990 ( 170) hydrogen bonds : angle 5.23517 ( 465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 39 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: B 622 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6786 (pmm) REVERT: B 662 ARG cc_start: 0.6232 (OUTLIER) cc_final: 0.5961 (tpm170) REVERT: B 725 LEU cc_start: 0.7138 (tp) cc_final: 0.6843 (tt) REVERT: B 732 TYR cc_start: 0.3820 (OUTLIER) cc_final: 0.2585 (m-80) outliers start: 29 outliers final: 16 residues processed: 61 average time/residue: 0.0447 time to fit residues: 3.7555 Evaluate side-chains 57 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 833 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.083130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.072464 restraints weight = 26486.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.074070 restraints weight = 15732.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.075259 restraints weight = 10861.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.076061 restraints weight = 8155.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.076580 restraints weight = 6597.770| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5680 Z= 0.162 Angle : 0.581 13.272 7744 Z= 0.290 Chirality : 0.044 0.140 900 Planarity : 0.004 0.040 962 Dihedral : 8.458 73.125 839 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.26 % Allowed : 33.96 % Favored : 60.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.31), residues: 680 helix: 0.07 (0.38), residues: 195 sheet: -2.13 (0.41), residues: 146 loop : -1.61 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 504 TYR 0.016 0.001 TYR B 575 PHE 0.016 0.002 PHE B 470 TRP 0.006 0.001 TRP B 823 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5680) covalent geometry : angle 0.58137 ( 7744) hydrogen bonds : bond 0.04245 ( 170) hydrogen bonds : angle 5.30958 ( 465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 38 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: B 222 LYS cc_start: 0.8042 (pttp) cc_final: 0.7723 (tptm) REVERT: B 430 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.8009 (t-90) REVERT: B 476 PHE cc_start: 0.6731 (OUTLIER) cc_final: 0.5780 (m-80) REVERT: B 622 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.7020 (pmm) REVERT: B 662 ARG cc_start: 0.6442 (OUTLIER) cc_final: 0.6119 (tpm170) REVERT: B 732 TYR cc_start: 0.4317 (OUTLIER) cc_final: 0.3091 (m-80) outliers start: 31 outliers final: 21 residues processed: 63 average time/residue: 0.0610 time to fit residues: 5.4119 Evaluate side-chains 61 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 35 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 476 PHE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 833 CYS Chi-restraints excluded: chain B residue 855 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.081851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.071344 restraints weight = 26247.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.072945 restraints weight = 15885.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.074061 restraints weight = 11066.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.074901 restraints weight = 8422.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.075479 restraints weight = 6783.450| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5680 Z= 0.198 Angle : 0.608 13.617 7744 Z= 0.303 Chirality : 0.044 0.143 900 Planarity : 0.004 0.039 962 Dihedral : 8.542 73.215 839 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.26 % Allowed : 32.94 % Favored : 61.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.31), residues: 680 helix: -0.11 (0.38), residues: 198 sheet: -2.23 (0.40), residues: 147 loop : -1.76 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 702 TYR 0.017 0.001 TYR B 575 PHE 0.017 0.002 PHE B 470 TRP 0.007 0.001 TRP B 823 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 5680) covalent geometry : angle 0.60781 ( 7744) hydrogen bonds : bond 0.04378 ( 170) hydrogen bonds : angle 5.37906 ( 465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 35 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 430 HIS cc_start: 0.8559 (OUTLIER) cc_final: 0.8118 (t-90) REVERT: B 476 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.5799 (m-80) REVERT: B 732 TYR cc_start: 0.4246 (OUTLIER) cc_final: 0.3037 (m-80) outliers start: 31 outliers final: 21 residues processed: 63 average time/residue: 0.0590 time to fit residues: 5.1374 Evaluate side-chains 58 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 34 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 476 PHE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 833 CYS Chi-restraints excluded: chain B residue 855 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 67 optimal weight: 0.0570 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.083500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.073014 restraints weight = 25924.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.074649 restraints weight = 15404.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.075871 restraints weight = 10569.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.076636 restraints weight = 7940.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.077270 restraints weight = 6432.259| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5680 Z= 0.112 Angle : 0.577 13.291 7744 Z= 0.277 Chirality : 0.043 0.142 900 Planarity : 0.004 0.039 962 Dihedral : 8.325 73.224 839 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.92 % Allowed : 33.96 % Favored : 61.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.31), residues: 680 helix: 0.09 (0.38), residues: 201 sheet: -2.24 (0.40), residues: 151 loop : -1.72 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 504 TYR 0.014 0.001 TYR B 575 PHE 0.013 0.001 PHE B 470 TRP 0.009 0.001 TRP B 442 HIS 0.003 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 5680) covalent geometry : angle 0.57703 ( 7744) hydrogen bonds : bond 0.03597 ( 170) hydrogen bonds : angle 5.09568 ( 465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 36 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: B 222 LYS cc_start: 0.8327 (pttp) cc_final: 0.7857 (tptp) REVERT: B 257 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8575 (tp) REVERT: B 430 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.8072 (t-90) REVERT: B 732 TYR cc_start: 0.3872 (OUTLIER) cc_final: 0.2410 (m-80) outliers start: 29 outliers final: 20 residues processed: 62 average time/residue: 0.0406 time to fit residues: 3.5805 Evaluate side-chains 57 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 34 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 833 CYS Chi-restraints excluded: chain B residue 855 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.0030 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.082149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.071717 restraints weight = 25880.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.073299 restraints weight = 15618.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.074461 restraints weight = 10826.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.075262 restraints weight = 8212.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.075807 restraints weight = 6652.424| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5680 Z= 0.160 Angle : 0.591 13.653 7744 Z= 0.290 Chirality : 0.044 0.141 900 Planarity : 0.004 0.050 962 Dihedral : 8.378 73.168 839 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.41 % Allowed : 34.30 % Favored : 61.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.31), residues: 680 helix: 0.12 (0.38), residues: 198 sheet: -2.29 (0.40), residues: 151 loop : -1.68 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 662 TYR 0.014 0.001 TYR B 575 PHE 0.015 0.002 PHE B 470 TRP 0.006 0.001 TRP B 823 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5680) covalent geometry : angle 0.59102 ( 7744) hydrogen bonds : bond 0.03975 ( 170) hydrogen bonds : angle 5.20502 ( 465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 34 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: B 222 LYS cc_start: 0.8311 (pttp) cc_final: 0.7809 (tptp) REVERT: B 257 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8651 (tp) REVERT: B 430 HIS cc_start: 0.8536 (OUTLIER) cc_final: 0.8158 (t-90) REVERT: B 476 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.5786 (m-80) REVERT: B 732 TYR cc_start: 0.4011 (OUTLIER) cc_final: 0.2507 (m-80) outliers start: 26 outliers final: 20 residues processed: 58 average time/residue: 0.0685 time to fit residues: 5.5829 Evaluate side-chains 55 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 31 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 476 PHE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 833 CYS Chi-restraints excluded: chain B residue 855 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 38 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.082755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.072350 restraints weight = 25913.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.073948 restraints weight = 15468.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.075119 restraints weight = 10702.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.075922 restraints weight = 8108.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.076533 restraints weight = 6550.801| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5680 Z= 0.122 Angle : 0.577 13.447 7744 Z= 0.278 Chirality : 0.043 0.145 900 Planarity : 0.004 0.056 962 Dihedral : 8.271 73.235 839 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.75 % Allowed : 33.96 % Favored : 61.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.31), residues: 680 helix: 0.28 (0.38), residues: 198 sheet: -2.09 (0.41), residues: 144 loop : -1.70 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 662 TYR 0.014 0.001 TYR B 575 PHE 0.012 0.001 PHE B 470 TRP 0.008 0.001 TRP B 442 HIS 0.003 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5680) covalent geometry : angle 0.57727 ( 7744) hydrogen bonds : bond 0.03610 ( 170) hydrogen bonds : angle 5.09633 ( 465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 36 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: B 222 LYS cc_start: 0.8338 (pttp) cc_final: 0.7865 (mmtt) REVERT: B 257 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8606 (tp) REVERT: B 430 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.8119 (t-90) REVERT: B 523 MET cc_start: 0.7593 (pmm) cc_final: 0.7298 (pmm) REVERT: B 732 TYR cc_start: 0.3968 (OUTLIER) cc_final: 0.2513 (m-80) outliers start: 28 outliers final: 22 residues processed: 61 average time/residue: 0.0419 time to fit residues: 3.5626 Evaluate side-chains 59 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 34 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 833 CYS Chi-restraints excluded: chain B residue 855 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 31 optimal weight: 0.0040 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.083560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.073127 restraints weight = 25950.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.074765 restraints weight = 15466.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.075923 restraints weight = 10677.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.076723 restraints weight = 8054.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.077320 restraints weight = 6506.895| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5680 Z= 0.108 Angle : 0.573 13.245 7744 Z= 0.273 Chirality : 0.043 0.146 900 Planarity : 0.004 0.060 962 Dihedral : 8.178 73.229 839 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.24 % Allowed : 34.63 % Favored : 61.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.31), residues: 680 helix: 0.53 (0.39), residues: 195 sheet: -2.05 (0.41), residues: 146 loop : -1.59 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 662 TYR 0.012 0.001 TYR B 575 PHE 0.011 0.001 PHE B 470 TRP 0.009 0.001 TRP B 442 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 5680) covalent geometry : angle 0.57268 ( 7744) hydrogen bonds : bond 0.03358 ( 170) hydrogen bonds : angle 4.97833 ( 465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 34 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: B 128 TRP cc_start: 0.7315 (OUTLIER) cc_final: 0.6645 (t60) REVERT: B 222 LYS cc_start: 0.8313 (pttp) cc_final: 0.7839 (mmtt) REVERT: B 257 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8601 (tp) REVERT: B 430 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.8185 (t-90) REVERT: B 732 TYR cc_start: 0.3902 (OUTLIER) cc_final: 0.2491 (m-80) outliers start: 25 outliers final: 19 residues processed: 56 average time/residue: 0.0426 time to fit residues: 3.5748 Evaluate side-chains 56 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 33 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 833 CYS Chi-restraints excluded: chain B residue 855 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.083334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.072912 restraints weight = 25895.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.074555 restraints weight = 15465.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.075734 restraints weight = 10681.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.076481 restraints weight = 8057.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.077097 restraints weight = 6552.822| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5680 Z= 0.117 Angle : 0.577 13.096 7744 Z= 0.276 Chirality : 0.043 0.151 900 Planarity : 0.004 0.065 962 Dihedral : 8.178 73.237 839 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.75 % Allowed : 33.62 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.31), residues: 680 helix: 0.58 (0.39), residues: 195 sheet: -2.07 (0.41), residues: 153 loop : -1.57 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 662 TYR 0.013 0.001 TYR B 575 PHE 0.012 0.001 PHE B 470 TRP 0.007 0.001 TRP B 442 HIS 0.004 0.001 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 5680) covalent geometry : angle 0.57677 ( 7744) hydrogen bonds : bond 0.03460 ( 170) hydrogen bonds : angle 4.95810 ( 465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 892.54 seconds wall clock time: 16 minutes 13.92 seconds (973.92 seconds total)